Hi When I run this code: LunSpikeInDat

What's the output of running BiocManager::valid() ?<br

This is the output of BiocManager::valid( ) : <di

Thank you! <a class="user-mention notranslate" data-hovercard-type="user" data-hoverca

Problem in downloading LunSpikeInData about orchestratingsinglecellanalysis HOT 7 CLOSED

MAmin99m commented on June 16, 2024

Problem in downloading LunSpikeInData

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Comments (7)

LTLA commented on June 16, 2024 2

FYI you can force re-download of potentially corrupted cache elements with

ehub <- ExperimentHub()
ehub[["EH2674", force=TRUE]]

Assumes that the sqlite file itself is not corrupted, in which case nuking the entire directory is the only way.

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MAmin99m commented on June 16, 2024 1

I think you're right because after removing the contents of.cache/R/ExperimentHub I can use LunSpikeInData() without any problem.
Thanks for your help, Peter.

> suppressPackageStartupMessages(library(ExperimentHub))
> eh <- ExperimentHub(ask = FALSE)
snapshotDate(): 2022-04-26
> #> snapshotDate(): 2022-04-26
> eh["EH2674"]
ExperimentHub with 1 record
# snapshotDate(): 2022-04-26
# names(): EH2674
# package(): scRNAseq
# $dataprovider: ArrayExpress
# $species: Mus musculus
# $rdataclass: matrix
# $rdatadateadded: 2019-07-01
# $title: Lun 416B plus spike-in counts
# $description: Count matrix for the Lun 416B (plus spike-ins) single-cell RNA-seq dataset
# $taxonomyid: 10090
# $genome: mm10
# $sourcetype: TSV
# $sourceurl: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5522/
# $sourcesize: NA
# $tags: c("ExperimentHub", "ExperimentData", "ExpressionData", "SequencingData",
#   "RNASeqData") 
# retrieve record with 'object[["EH2674"]]' 
> str(eh[["EH2674"]])
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
 int [1:46703, 1:192] 0 0 0 0 0 0 0 0 0 0 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:46703] "ENSMUSG00000102693" "ENSMUSG00000064842" "ENSMUSG00000051951" "ENSMUSG00000102851" ...
  ..$ : chr [1:192] "SLX-9555.N701_S502.C89V9ANXX.s_1.r_1" "SLX-9555.N701_S503.C89V9ANXX.s_1.r_1" "SLX-9555.N701_S504.C89V9ANXX.s_1.r_1" "SLX-9555.N701_S505.C89V9ANXX.s_1.r_1" ...

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PeteHaitch commented on June 16, 2024 1

Great, happy to help @mamalek99

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PeteHaitch commented on June 16, 2024

What's the output of running BiocManager::valid()?
I just tested this and it worked for me on the following system (this is the current release version of Bioconductor albeit with some slightly out-of-date packages):

> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org


* sessionInfo()

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8       
 [4] LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] ensembldb_2.20.1            AnnotationFilter_1.20.0     GenomicFeatures_1.48.1     
 [4] AnnotationDbi_1.58.0        scRNAseq_2.10.0             SingleCellExperiment_1.18.0
 [7] SummarizedExperiment_1.26.1 Biobase_2.56.0              GenomicRanges_1.48.0       
[10] GenomeInfoDb_1.32.2         IRanges_2.30.0              S4Vectors_0.34.0           
[13] BiocGenerics_0.42.0         MatrixGenerics_1.8.0        matrixStats_0.62.0         

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.28.0           bitops_1.0-7                  bit64_4.0.5                  
 [4] filelock_1.0.2                progress_1.2.2                httr_1.4.3                   
 [7] tools_4.2.1                   utf8_1.2.2                    R6_2.5.1                     
[10] DBI_1.1.3                     lazyeval_0.2.2                tidyselect_1.1.2             
[13] prettyunits_1.1.1             bit_4.0.4                     curl_4.3.2                   
[16] compiler_4.2.1                cli_3.3.0                     xml2_1.3.3                   
[19] DelayedArray_0.22.0           rtracklayer_1.56.0            rappdirs_0.3.3               
[22] stringr_1.4.0                 digest_0.6.29                 Rsamtools_2.12.0             
[25] bspm_0.3.9                    XVector_0.36.0                pkgconfig_2.0.3              
[28] htmltools_0.5.2               dbplyr_2.2.1                  fastmap_1.1.0                
[31] rlang_1.0.4                   rstudioapi_0.13               RSQLite_2.2.14               
[34] shiny_1.7.1                   BiocIO_1.6.0                  generics_0.1.3               
[37] BiocParallel_1.30.0           dplyr_1.0.9                   RCurl_1.98-1.7               
[40] magrittr_2.0.3                GenomeInfoDbData_1.2.8        Matrix_1.4-1                 
[43] Rcpp_1.0.9                    fansi_1.0.3                   lifecycle_1.0.1              
[46] stringi_1.7.8                 yaml_2.3.5                    zlibbioc_1.42.0              
[49] BiocFileCache_2.4.0           AnnotationHub_3.4.0           grid_4.2.1                   
[52] blob_1.2.3                    parallel_4.2.1                promises_1.2.0.1             
[55] ExperimentHub_2.4.0           crayon_1.5.1                  lattice_0.20-45              
[58] Biostrings_2.64.0             hms_1.1.1                     KEGGREST_1.36.0              
[61] pillar_1.7.0                  rjson_0.2.21                  biomaRt_2.52.0               
[64] XML_3.99-0.9                  glue_1.6.2                    BiocVersion_3.15.2           
[67] BiocManager_1.30.18           png_0.1-7                     vctrs_0.4.1                  
[70] httpuv_1.6.5                  purrr_0.3.4                   assertthat_0.2.1             
[73] cachem_1.0.6                  mime_0.12                     xtable_1.8-4                 
[76] restfulr_0.0.13               later_1.3.0                   tibble_3.1.7                 
[79] GenomicAlignments_1.32.0      memoise_2.0.1                 ellipsis_0.3.2               
[82] interactiveDisplayBase_1.34.0

Bioconductor version '3.15'

  * 35 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "BiocParallel", "edgeR", "ensembldb", "GenomicFeatures", "gtools", "HDF5Array", "htmltools", "igraph",
    "KEGGREST", "limma", "lme4", "locfit", "MatrixGenerics", "pillar", "R.methodsS3", "R.oo", "R.utils",
    "RcppHNSW", "restfulr", "reticulate", "rgl", "Rhdf5lib", "RSQLite", "rtracklayer", "scuttle", "shiny",
    "shinyWidgets", "tidyverse", "XML"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

from orchestratingsinglecellanalysis.

MAmin99m commented on June 16, 2024

This is the output of BiocManager::valid( ) :

> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org


* sessionInfo()

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] scRNAseq_2.10.0             SingleCellExperiment_1.18.0 SummarizedExperiment_1.26.1
 [4] Biobase_2.56.0              GenomicRanges_1.48.0        GenomeInfoDb_1.32.2        
 [7] IRanges_2.30.0              MatrixGenerics_1.8.1        matrixStats_0.62.0         
[10] BiocFileCache_2.4.0         dbplyr_2.2.1                S4Vectors_0.34.0           
[13] BiocGenerics_0.42.0        

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.28.0           bitops_1.0-7                  bit64_4.0.5                  
 [4] filelock_1.0.2                progress_1.2.2                httr_1.4.3                   
 [7] tools_4.2.1                   utf8_1.2.2                    R6_2.5.1                     
[10] DBI_1.1.3                     lazyeval_0.2.2                tidyselect_1.1.2             
[13] prettyunits_1.1.1             bit_4.0.4                     curl_4.3.2                   
[16] compiler_4.2.1                cli_3.3.0                     xml2_1.3.3                   
[19] DelayedArray_0.22.0           rtracklayer_1.56.1            rappdirs_0.3.3               
[22] stringr_1.4.0                 digest_0.6.29                 Rsamtools_2.12.0             
[25] XVector_0.36.0                pkgconfig_2.0.3               htmltools_0.5.3              
[28] fastmap_1.1.0                 ensembldb_2.20.2              rlang_1.0.4                  
[31] rstudioapi_0.13               RSQLite_2.2.15                shiny_1.7.2                  
[34] BiocIO_1.6.0                  generics_0.1.3                BiocParallel_1.30.3          
[37] dplyr_1.0.9                   RCurl_1.98-1.7                magrittr_2.0.3               
[40] GenomeInfoDbData_1.2.8        Matrix_1.4-1                  Rcpp_1.0.9                   
[43] fansi_1.0.3                   lifecycle_1.0.1               stringi_1.7.8                
[46] yaml_2.3.5                    zlibbioc_1.42.0               AnnotationHub_3.4.0          
[49] grid_4.2.1                    blob_1.2.3                    parallel_4.2.1               
[52] promises_1.2.0.1              ExperimentHub_2.4.0           crayon_1.5.1                 
[55] lattice_0.20-45               Biostrings_2.64.0             GenomicFeatures_1.48.3       
[58] hms_1.1.1                     KEGGREST_1.36.3               pillar_1.8.0                 
[61] rjson_0.2.21                  codetools_0.2-18              biomaRt_2.52.0               
[64] XML_3.99-0.10                 glue_1.6.2                    BiocVersion_3.15.2           
[67] BiocManager_1.30.18           png_0.1-7                     vctrs_0.4.1                  
[70] httpuv_1.6.5                  purrr_0.3.4                   assertthat_0.2.1             
[73] cachem_1.0.6                  mime_0.12                     xtable_1.8-4                 
[76] restfulr_0.0.15               AnnotationFilter_1.20.0       later_1.3.0                  
[79] tibble_3.1.7                  GenomicAlignments_1.32.0      AnnotationDbi_1.58.0         
[82] memoise_2.0.1                 ellipsis_0.3.2                interactiveDisplayBase_1.34.0

Bioconductor version '3.15'

  * 1 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install("igraph", update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 0 packages too new

from orchestratingsinglecellanalysis.

PeteHaitch commented on June 16, 2024

Hmm, nothing obviously wrong there.
I suspect it might be due to a problem with your ExperimentHub installation (ExperimentHub is the underlying package responsible for data downloading and caching).
Let's try accessing that resource directory from ExperimentHub; what does this code return on your machine:

suppressPackageStartupMessages(library(ExperimentHub))
eh <- ExperimentHub(ask = FALSE)
#> snapshotDate(): 2022-04-26
eh["EH2674"]
#> ExperimentHub with 1 record
#> # snapshotDate(): 2022-04-26
#> # names(): EH2674
#> # package(): scRNAseq
#> # $dataprovider: ArrayExpress
#> # $species: Mus musculus
#> # $rdataclass: matrix
#> # $rdatadateadded: 2019-07-01
#> # $title: Lun 416B plus spike-in counts
#> # $description: Count matrix for the Lun 416B (plus spike-ins) single-cell R...
#> # $taxonomyid: 10090
#> # $genome: mm10
#> # $sourcetype: TSV
#> # $sourceurl: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5522/
#> # $sourcesize: NA
#> # $tags: c("ExperimentHub", "ExperimentData", "ExpressionData",
#> #   "SequencingData", "RNASeqData") 
#> # retrieve record with 'object[["EH2674"]]'
str(eh[["EH2674"]])
#> see ?scRNAseq and browseVignettes('scRNAseq') for documentation
#> loading from cache
#>  int [1:46703, 1:192] 0 0 0 0 0 0 0 0 0 0 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ : chr [1:46703] "ENSMUSG00000102693" "ENSMUSG00000064842" "ENSMUSG00000051951" "ENSMUSG00000102851" ...
#>   ..$ : chr [1:192] "SLX-9555.N701_S502.C89V9ANXX.s_1.r_1" "SLX-9555.N701_S503.C89V9ANXX.s_1.r_1" "SLX-9555.N701_S504.C89V9ANXX.s_1.r_1" "SLX-9555.N701_S505.C89V9ANXX.s_1.r_1" ...

^{Created on 2022-07-21 by the reprex package (v2.0.1)}

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MAmin99m commented on June 16, 2024

Thank you! @LTLA

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Problem in downloading LunSpikeInData about orchestratingsinglecellanalysis HOT 7 CLOSED

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